20.309 development to-do list
20.309:Course Information
20.309:DAQ System
20.309:Homeworks/Homework 3
20.309:Lab Report Guidelines
20.309:Learning outcomes
20.309:Safety
20.345: Wiki guidelines
20.345:Course Information
20.345:Final project proposal
20.345:Key Factors Table
20.345:Literature search
20.345:Main page
==Weekly Progress Reports==
A.Williams: Objectives and Literature Review
AFM
ANOID Project
Additional Resources
Aligning the optical trap
Alumni Page
BE Classroom Computer Documentation
Bode plots and frequency response
CM March14
CM March28
Capacitors and inductors
Cartridge Manipulation
Category:20.309 General Information
Category:20.345
Cell Printing
Cell Printing Experimentation
Cell Reservations
Cellular microrheology
Confocal Wiki
Converting Gaussian fit to Rayleigh resolution
Course Journal -- Nathan S Lachenmyer
Coursework
DNA Melter Improvements
DNA Melting
DNA Melting II: Using the Matlab DNALockIn GUI
DNA Melting Part 1: Measuring Temperature and Fluorescence
DNA Melting Part 1: Simulating DNA Melting - Basics
DNA Melting Part 2: Lock-in Amplifier and Temperature Control
DNA Melting Part 2: Measuring Temperature and Fluorescence
DNA Melting Part 3: Simulating DNA Melting - Intermediate Topcs
DNA Melting Part 3: Simulating DNA Melting - Intermediate Topics
DNA Melting Part 4: Lock-in Amplifier and Temperature Control
DNA Melting Part 5: Multi-parameter Data Analysis
DNA Melting Report Requirements
DNA Melting Report Requirements for Part 1
DNA Melting Report Requirements for Part 2
DNA Melting Thermodynamics
DNA Melting: DNA Sequences
DNA Melting: Model function and parameter estimation by nonlinear regression
DNA Melting: Processing DNA Melting Data
DNA Melting: Simulating DNA Melting - Basics
DNA Melting: Simulating DNA Melting - Intermediate Topics
DNA Melting: Using the Basic DNAMelter GUI
DNA Melting: Using the LockIn DNAMelter GUI
DNA Melting: Using the Matlab DNAMelter GUI
DNA melting lab wiki pages
Data Sheets
Deconvolved Image
Device Creation
Discussion
ESTORM
Electronics Mini-Lab
Electronics Module
Electronics Primer
Electronics primer
Emmanuel Quiroz
Equipment on loan
Error analysis
FPGA Design Environment
Fall 2010 Syllabus
Fall 2010: DNA melting report outline
Fall 2010: Microscopy report outline
Fall 2010: Problem Set 3
Fall 2012: Journal Presentations
Final Project -- Nathan S Lachenmyer
Final Project Proposal Williams
Final Project: Spatial Light Modulator Galore
Final Projects
Fluorescence Imaging of Actin Cytoskeleton
Geometrical Optics
Geometrical optics and ray tracing
Hattie Chung
Image processing
Inkjet Technologies
Intro Electronics Lab Report
Introduction
Key Project Elements
Key estimates
Lab 1 Report -- Nathan S Lachenmyer
Lab 2 Report -- Nathan S Lachenmyer
Lab Manual: Atomic Force Microscopy (AFM)
Lab Manual: Limits of Detection
Lab Manual: Measuring DNA Melting Curves
Lab Manual: Optical Microscopy
Lab Manual:Atomic Force Microscopy (AFM)
Lab Manual:Intro to electronics
Lab Manual:Introduction to electronics
Lab Manual:Measuring DNA Melting Curves
Lab Manual:Optical Microscopy
Lab Manual:Optical Trapping
Lab Manual:Processing DNA Melting Data
Lab Report Guidelines
Lecture Notes:Modeling real systems with ideal elements
Limits of Detection: Data Sessions
Limits of Detection: Lab Manual
Limits of Detection:Report Requirements
Locating objects in a fluorescent microscopic image
MATLAB: Estimating resolution from a PSF slide image
MATLAB: Estimating viscoelastic spectrum using Mason's method
MRI lab: FPGA controller documentation
Main Page
March14
Matlab: Simulating Brownian motion
Matlab:DNA Melting Data Analysis
Matlab:DNA melting data analysis
Matlab:Division operators
Matlab:Image Processing for Fluorescent Microscopy
Matlab:Matlab Fundamentals
Matlab:Simulating DNA Melting
Matlab:Simulating DNA melting
Measuring optical magnification
Methods
Microrheology Measurements via Particle Tracking
Microscope Objective Lenses
Microscopy report outline
More info on BJC2100 Attempt
Nonlinear regression
Objective
Optical Microscopy Data Sheets
Optical Microscopy Part 1: Bright Field Microscopy
Optical Microscopy Part 1: Brightfield Microscopy
Optical Microscopy Part 1b: Geometrical Optics and Ray Tracing
Optical Microscopy Part 1b: Ray Tracing
Optical Microscopy Part 1c: Physical Optics and Limits of Detection
Optical Microscopy Part 1d: Noise Sources in Light Detection
Optical Microscopy Part 2: Fluorescence Microscopy
Optical Microscopy Part 2b: High Resolution Microscopy Techniques
Optical Microscopy Part 3: Particle Tracking
Optical Microscopy Part 3: Particle Tracking Applications
Optical Microscopy Part 3: Resolution and Stability
Optical Microscopy Part 3a: Particle Tracking
Optical Microscopy Part 3a: Particle Tracking in Glycerin Samples
Optical Microscopy Part 3b: Microrheology Measurements in Fibroblast Cells
Optical Microscopy Part 3b: Microrheology Measurements in Live Fibroblast Cells
Optical Microscopy Part 3c: Fluorescence Imaging of Actin Cytoskeleton
Optical Microscopy Part 3c: Protocols for cell culture, cell fixing and cell imaging
Optical Microscopy Part 4: Microrheology Measurements in Fibroblast Cells
Optical Microscopy Part 4: Particle Tracking
Optical Microscopy Week 1: Bright Field Microscopy
Optical Microscopy Week 1: Brightfield Microscopy
Optical Microscopy Week 1: Build a brightfield microscope
Optical Microscopy Week 2: Add a fluorescence branch
Optical Microscopy Week 2: Fluorescence Microscopy
Optical Microscopy Week 3: Experiments
Optical Microscopy Week 3: Particle Tracking
Optical Microscopy Week 4: Microrheology Measurements in Fibroblast Cells
Optical Microscopy: Brownian motion and microscope stability
Optical Microscopy: Brownian motion and microscopy stability
Optical Microscopy: Construction of a microscope
Optical Microscopy: Fluorescence Microscopy
Optical Microscopy: Part 1 Report Outline
Optical Microscopy: Part 2 Report Outline
Optical Microscopy: Part 3 Report Outline
Optical Microscopy: Part 4 Report Outline
Optical Trap Code
Optical Trap Graphs
Optical detectors, noise, and the limit of detection
Optical microscopy lab wiki pages
Optical resolution
Optical trap
Papers
Papers to read
Photobleaching Model
Physical optics and resolution
Probability and statistics
Problem Set 1
Problem Set 2
Problem Set 2 Fall 2010
Procedure: Diffusion in biological gels
Procedure: Particle tracking
Procedure: Peptide-DNA Tethering Assay
Project ideas
Protocols
Protocols for cell culture
Protocols for cell culture, fixing and imaging
Python:DNA melting data analysis
Python:Simulating DNA Melting
QRT-PCR
QRT-PCR:Get Started
QRT-PCR:Heated Lid
QRT-PCR:LabView-versions
Real electronics
Reference List
Resource List:Electronics
Resource List:Suppliers
Resource list: DNA melting and PCR
Resource list: Electronics
Resource list: Fiber optics
Resource list: Image Enhancement
Resource list: Image processing
Resource list: Magnetic Resonance Imaging
Resource list: Matlab
Resource list: Microscopy
Resource list: Optical trapping
Resource list: Optics
Resource list: Particle tracking
Resource list: Suppliers
Resource list:DNA melting and PCR
Resource list:Electronics
Resource list:Magnetic Resonance Imaging
Resource list:Optical trapping
Resource list:Optics
Resource list:Suppliers
Results
Sandbox
Shot noise and centroid finding
Simulating diffusing microspheres in MATLAB
Spring 11 Chemotaxis Assay Weekly Reports
Spring 11 ChemotaxisAssayWeeklyReports
Spring 11:CellPrinter
Spring 11:Chemotaxis Assay
Spring 11:Confocal Microscope
Spring 11:Directed Evolution
Spring 11:Directed Evolution/KAF95
Spring 11:Directed Evolution/Perfusion Chambers
Spring 11:Directed Evolution/Week of 3-14-2011 Status
Spring 11:Directed Evolution/Week of 3-21-2011 Status
Spring 11:Directed Evolution/Week of 3-28-2011 Status
Spring 11:Directed Evolution/Week of 4-04-2011 Status
Spring 11:Directed Evolution/Week of 4-11-2011 Status
Spring 11:Directed Evolution/Week of 4-18-2011 Status
Spring 11:Directed Evolution/Week of 4-25-2011 Status
Spring 11:Directed Evolution/Week of 5-02-2011 Status
Spring 11:Directed Evolution/Week of 5-09-2011 Status
Spring 11:QRT-PCR
Spring 11:QRT-PCR weekly reports
Spring 11:QRT-PCR: Progress Notes
Spring 11:SMR
Spring 11:eSTORM
Spring 2011:3D PSF lab
Spring 2011:3D PSF lab:Kristin
Spring 2011:CellFinder
Spring 2011:Optical Trapping Lab
Spring 2012 Bioinstrumentation Project Lab
Spring 2012 Bioinstrumentation Project Lab.
Spring 2012: Ajoke Jumoke Williams
Spring 2012: Jonathan Gootenberg
Spring 2012: Jonathan Gootenberg FinProject
Spring 2012: Jonathan Gootenberg Journal
Spring 2012: Jonathan Gootenberg Lab 2
Spring 2012: Jonathan Gootenberg STORM
Spring 2012: Real Time qPCR
Spring 2012: Vincent Lee
Spring 2012: Williams Key Factors Table
Spring 2012:LFM
Spring 2012:LFM Documentation
Spring 2012:LFM Extra
Spring 2012:LFM Literature
Spring 2012:LFM Proposal
Spring 2012:LFM Report
Spring 2012:Leanna Morinishi
Spring 2012:Leanna Morinishi Journal
Spring 2012:Leanna Morinishi LFM
Spring 2012:Leanna Morinishi Lab 1
Spring 2012:Leanna Morinishi Lab 2
Spring 2012:Leanna Morinishi Lit Search
Spring 2012:PSF lab
Spring 2012:Snot
Spring 2012:Vincent Lee Journal
Spring 2012:Vincent Lee Lab 1
Spring 2012:Vincent Lee Lab 2
Spring09/Todo
Spring09:Todo list
Statement of Interest
Status Report Interrogatories (Spring 2012)
Super resolution microscopy
TableTop MRI
Talk:DNA Melting Part 1: Measuring Temperature and Fluorescence
Talk:DNA Melting: Simulating DNA Melting - Basics
Talk:Electronics Mini-Lab
Talk:Electronics Module
Talk:Lab Manual: Measuring DNA Melting Curves
Talk:Main Page
Talk:Optical Microscopy Part 2: Fluorescence Microscopy
Talk:Williams: Optical Trapping Lab 1
Technical Writing
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Template:Biohazard warning
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Template:Environmental Warning
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Template:Leanna20.345
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Template:LectureEquation
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Template:Math
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Template:MatlabDocumentationLink
Template:Note
Template:PrecisionMeasurement
Template:Safety Warning
Template:TechTV
Theory
Thermal Quenching Model
ThorLabs OTKB optical trapping kit
Todo List
Troubleshooting
User talk:Afrah Shafqat
User talk:Afrah Shafquat
User talk:Agi Stachowiak
User talk:Aislyn
User talk:Ajoke Williams
User talk:Alexa Schulte
User talk:Alvin Chen
User talk:Amneet
User talk:Amneet Gulati
User talk:Angel Rubio
User talk:Angela Zhu
User talk:Anirudh Arun
User talk:Anne Ye
User talk:Asmamaw Wassie
User talk:Ben Johnson
User talk:Benjamin Johnson
User talk:Brett Boval
User talk:Brian Djaja
User talk:Brian Jude Joseph
User talk:Brian Ross
User talk:Brigitte Morales
User talk:Bweh Esembeson
User talk:Cara Brown
User talk:Catherine Fan
User talk:Charles Mitchell
User talk:Christian Wentz
User talk:Clarissa Zimmerman
User talk:Colin Beckwitt
User talk:Cory Li
User talk:Cuong450
User talk:Daniel Glover
User talk:Dguggian
User talk:Divya Arcot
User talk:Divya Chhabra
User talk:Edgar Matias
User talk:Eliot Frank
User talk:Elizabeth Choe
User talk:Elizabeth Rowland
User talk:Emily
User talk:Emily Brown
User talk:Emmanuel Quiroz
User talk:Evets Namresaw
User talk:Faith OBrian
User talk:Fangdi Sun
User talk:Forea Wang
User talk:Gabriella de Paz
User talk:Giulia Dula
User talk:Grant Robinson
User talk:Gustavo Goretkin
User talk:Hannah Johnsen
User talk:Holly Chamberlain
User talk:Huayu Ding
User talk:Iris Sheu
User talk:Jacqueline Soegaard
User talk:Jamal Elkhader
User talk:Jchien
User talk:Jenn Lai
User talk:Jeremy Chang
User talk:Jessica Li
User talk:Jessica Perez
User talk:Jingkun Yang
User talk:Joanna Yeh
User talk:John Chen
User talk:Jonathan Gootenberg
User talk:Justin
User talk:Kelly Drinkwater
User talk:Kevin Hu
User talk:Kristen Wilhite
User talk:Kristin Kuhn
User talk:Krithi Sundaram
User talk:Laura Seaman
User talk:Lauren Berry
User talk:Leanna Morinishi
User talk:Logan Williams
User talk:Luis Juarez
User talk:MAXINE JONAS
User talk:Mariana Duran
User talk:Masahiro Yamaguchi
User talk:Matthew Hung
User talk:Max (Chung-an) Wu
User talk:Max Pruner
User talk:Meghan Nelson
User talk:Melina Tsitsiklis
User talk:Michael Hwang
User talk:Michael Meyer
User talk:Nahum Seifeselassie
User talk:Nathan S Lachenmyer
User talk:Nidharshan Anandasivam
User talk:Nina Jreige
User talk:Oliver Lieleg
User talk:Paula Trepmahn
User talk:Paula Trepman
User talk:Pei-Ann Lin
User talk:Philip Smith
User talk:Queenie Chan
User talk:Ranbel Sun
User talk:Robert McIntyre
User talk:Ruisi Shang
User talk:Ryan Keating
User talk:Sabina Sood
User talk:Samantha Alvarez
User talk:Samira Daswani
User talk:Scott manalis
User talk:Sebastian Lukjan
User talk:Shireen Rudina
User talk:Shirley Galbiati
User talk:Sivakami Sambasivam
User talk:Steph Leger
User talk:Stephanie Bachar
User talk:Stephanie Fung
User talk:Steven Carreno
User talk:Steven Nagle
User talk:Tonia Tsinman
User talk:Vincent Lee
User talk:William Hesse
User talk:William Morejon
User talk:Xinqi Li
User talk:Yimin Chen
User talk:Zach Banks
User:Afrah Shafqat
User:Afrah Shafquat
User:Agi Stachowiak
User:Aislyn
User:Ajoke Williams
User:Alexa Schulte
User:Alvin Chen
User:Amneet
User:Amneet Gulati
User:Angel Rubio
User:Angela Zhu
User:Anirudh Arun
User:Anne Ye
User:Asmamaw Wassie
User:Ben Johnson
User:Benjamin Johnson
User:Brett Boval
User:Brian Djaja
User:Brian Jude Joseph
User:Brian Ross
User:Brigitte Morales
User:Bweh Esembeson
User:Cara Brown
User:Catherine Fan
User:Charles Mitchell
User:Christian Wentz
User:Clarissa Zimmerman
User:Colin Beckwitt
User:Cory Li
User:Cuong450
User:Daniel Glover
User:Dguggian
User:Divya Arcot
User:Divya Chhabra
User:Edgar Matias
User:Eliot Frank
User:Elizabeth Choe
User:Elizabeth Rowland
User:Emily
User:Emily Brown
User:Emmanuel Quiroz
User:Evets Namresaw
User:Faith OBrian
User:Fangdi Sun
User:Forea Wang
User:Gabriella de Paz
User:Giulia Dula
User:Grant Robinson
User:Gustavo Goretkin
User:Hannah Johnsen
User:Holly Chamberlain
User:Huayu Ding
User:Iris Sheu
User:Jacqueline Soegaard
User:Jamal Elkhader
User:Jchien
User:Jenn Lai
User:Jeremy Chang
User:Jessica Li
User:Jessica Perez
User:Jingkun Yang
User:Joanna Yeh
User:John Chen
User:Jonathan Gootenberg
User:Justin
User:Kelly Drinkwater
User:Kevin Hu
User:Kristen Wilhite
User:Kristin Kuhn
User:Krithi Sundaram
User:Laura Seaman
User:Lauren Berry
User:Leanna Morinishi
User:Logan Williams
User:Luis Juarez
User:MAXINE JONAS
User:Mariana Duran
User:Masahiro Yamaguchi
User:Matthew Hung
User:Max (Chung-an) Wu
User:Max Pruner
User:Meghan Nelson
User:Melina Tsitsiklis
User:Michael Hwang
User:Michael Meyer
User:Nahum Seifeselassie
User:Nathan S Lachenmyer
User:Nidharshan Anandasivam
User:Nina Jreige
User:Oliver Lieleg
User:Paula Trepmahn
User:Paula Trepman
User:Pei-Ann Lin
User:Philip Smith
User:Queenie Chan
User:Ranbel Sun
User:Robert McIntyre
User:Ruisi Shang
User:Ryan Keating
User:Sabina Sood
User:Samantha Alvarez
User:Samira Daswani
User:Scott manalis
User:Sebastian Lukjan
User:Shireen Rudina
User:Shirley Galbiati
User:Sivakami Sambasivam
User:Steph Leger
User:Stephanie Bachar
User:Stephanie Fung
User:Steven Carreno
User:Steven Nagle
User:Tonia Tsinman
User:Vincent Lee
User:William Hesse
User:William Morejon
User:Xinqi Li
User:Yimin Chen
User:Zach Banks
Weekly Progress Reports
Weekly Updates
Wikibodeplots.m
Williams: Optical Trapping Lab 1
Williams: PSF and Deconvolution Lab 2
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